Lecture Notes in Computer Science

Commenced Publication in 1973 Founding and Former Series Editors: Gerhard Goos, Juris Hartmanis, and Jan van Leeuwen

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Editorial Board
David Hutchison Lancaster University, UK Takeo Kanade Carnegie Mellon University, Pittsburgh, PA, USA Josef Kittler University of Surrey, Guildford, UK Jon M. Kleinberg Cornell University, Ithaca, NY, USA Alfred Kobsa University of California, Irvine, CA, USA Friedemann Mattern ETH Zurich, Switzerland John C. Mitchell Stanford University, CA, USA Moni Naor Weizmann Institute of Science, Rehovot, Israel Oscar Nierstrasz University of Bern, Switzerland C. Pandu Rangan Indian Institute of Technology, Madras, India Bernhard Steffen University of Dortmund, Germany Madhu Sudan Microsoft Research, Cambridge, MA, USA Demetri Terzopoulos University of California, Los Angeles, CA, USA Doug Tygar University of California, Berkeley, CA, USA Gerhard Weikum Max-Planck Institute of Computer Science, Saarbruecken, Germany

Ashish Goel Friedrich C. Simmel Petr Sosk (Eds.)

DNA Computing
14th International Meeting on DNA Computing, DNA14 Prague, Czech Republic, June 2-9, 2008 Revised Selected Papers

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Volume Editors Ashish Goel Management Science and Engineering, and Computer Science, Terman 311 Stanford University Stanford, CA, USA E-mail: ashishg@stanford.edu Friedrich C. Simmel Physics Department TU Munich Garching, Germany E-mail: simmel@ph.tum.de Petr Sosk Institute of Computer Science Faculty of Philosophy and Science Silesian University Opava, Czech Republic E-mail: petr.sosik@fpf.slu.cz

Library of Congress Control Number: 2009936573 CR Subject Classication (1998): F.1, I.2.9, I.2.11, F.2.2, J.3 LNCS Sublibrary: SL 1 Theoretical Computer Science and General Issues ISSN ISBN-10 ISBN-13 0302-9743 3-642-03075-0 Springer Berlin Heidelberg New York 978-3-642-03075-8 Springer Berlin Heidelberg New York

This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specically the rights of translation, reprinting, re-use of illustrations, recitation, broadcasting, reproduction on microlms or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. springer.com Springer-Verlag Berlin Heidelberg 2009 Printed in Germany Typesetting: Camera-ready by author, data conversion by Scientic Publishing Services, Chennai, India Printed on acid-free paper SPIN: 12625284 06/3180 543210

Preface

The 14th international meeting on DNA computation took place in the Czech Republic in Prague, June 29, 2008. During the last 14 years the DNA Computing meetings have been the key forum at the boundary between computer science, biochemistry and nanotechnology where the most recent results have been presented and their authors have met. Their scientic program includes mathematical foundations and theoretical study of DNA computing or biocomputing in general and recent experimental results in DNA nanotechnology, nanoscience and nanocomputing. It continues to be one of the most exciting interdisciplinary meetings, as exemplied by the diverse nature of contributions in this volume. The meeting began with tutorial talks by Friedrich Simmel (Molecular Biology for Computer Scientists), Nadrian Seeman (Structural DNA Nanotechnology), and Yasubumi Sakakibara (Formal Grammars for DNA Computation and Bioinformatics). During the meeting, a number of excellent keynote speakers gave an up-to-date overview of dierent aspects of DNA computing and biochemical information processing. Luca Cardelli talked about Molecules as Automata, while Niles Pierce gave an exciting talk entitled Molecular ChoreographyProgramming Nucleic Acid Self-Assembly and Disassembly Pathways. In a more biological talk, Laura Landweber discussed RNA-Guided, Epigenetic Programming and Re-programming of Genomic Information in Ciliates, and Ming Li gave an overview of Modern Homology Search. The meeting was concluded by a Nanoday with beautiful presentations by Christof Niemeyer, Kurt Gothelf, Andrew Ellington and David Pine. In total, the meeting was attended by 85 researchers from 14 countries from Asia, North America and Europe. The DNA14 Program Committee received a total number of 59 submissions, of which 25 were presented orally. Their topics included theoretical models of biomolecular computing, demonstrations of biomolecular computing processes, self-assembly systems, DNA nanostructures and nanomachines, biotechnological and other applications of DNA computing and other related themes. This proceedings volume contains improved versions of 15 papers selected from these oral contributions. We wish to express out gratitude to the members of the Program Committee, the local organizers, the sponsor Silesian University in Opava and the Steering Committee who made DNA14 a great success. November 2008 Ashish Goel Friedrich Simmel Petr Sos k

Organization

Program Committee
Ashish Goel (Co-chair) Friedrich Simmel (Co-chair) Martyn Amos Alessandra Carbone Ho-Lin Chen Mark Daley Russell Deaton Rudolf Freund Hendrik Jan Hoogeboom Jozef Kelemen Thomas LaBean Maurice Margenstern Yongli Mi Satoshi Murata Mitsunori Ogihara Ion Petre John A. Rose Yasubumi Sakakibara Lloyd Smith David Soloveichik Petr Sos k Andrew Turbereld Reidun Twarock Ron Weiss Bernard Yurke Byoung-Tak Zhang Stanford University, USA Technical University Munich, Germany Manchester Metropolitan University, UK Pierre et Marie Curie, France Stanford University, USA University of Western Ontario, Canada University of Arkansas, USA Technical University of Vienna, Austria Leiden University, The Netherlands Silesian University, Czech Republic Duke University, USA University of Metz, France Hong Kong University of Science and Technology, Hong Kong Tokyo Instute of Technology, Japan University of Rochester, USA University of Turku, Finland Ritsumeikan APU, Japan Keio University, Japan University of Wisconsin-Madison, USA California Institute of Technology, USA Silesian University in Opava, Czech Republic Oxford University, UK University of York, UK Princeton University, USA Boise State University, USA Seoul National University, Korea

Steering Committee
Lila Kari (Chair) Leonard Adleman Anne Condon Masami Hagiya Natasha Jonoska Chengde Mao Giancarlo Mauri Satoshi Murata University of Western Ontario, Canada University of Southern California, USA (honorary member) University of British Columbia, Canada University of Tokyo, Japan University of Southern Florida, USA Purdue University, USA University of Milan-Bicocca, Italy Tokyo Instute of Technology, Japan

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Organization

Gheorghe Paun John Reif Grzegorz Rozenberg Nadrian Seeman Andrew Tubereld Erik Winfree

Romanian Academy, Bucharest and Seville University, Spain Duke University, USA University of Leiden, The Netherlands New York University, USA Oxford University, UK California Institute of Technology, USA

Local Organizing Committee - Prague

Petr Sos (chair) k Michaela Aov c a Ludek Cienciala Lucie Ciencialov a Magdalena Chmelaov r a Alica Kelemenov a Sarka Vavrekov c a Milena Zeithamlov a Silesian University in Opava, Czech Silesian University in Opava, Czech Silesian University in Opava, Czech Silesian University in Opava, Czech Silesian University in Opava, Czech Silesian University in Opava, Czech Silesian University in Opava, Czech Action M Agency, Czech Republic Republic Republic Republic Republic Republic Republic Republic

Sponsors
Silesian University in Opava

Table of Contents
Experimental Validation of Signal Dependent Operation in Whiplash PCR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ken Komiya, Masayuki Yamamura, and John A. Rose Towards DNA Comparator: The Machine That Compares DNA Concentrations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Fumiaki Tanaka, Takashi Tsuda, and Masami Hagiya Construction of Photon-Fueled DNA Nanomachines by Tethering Azobenzenes as Engines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Xingguo Liang, Hidenori Nishioka, Nobutaka Takenaka, and Hiroyuki Asanuma Operon Structure Optimization by Random Self-assembly . . . . . . . . . . . . . Yusuke Nakagawa, Katsuyuki Yugi, Kenji Tsuge, Mitsuhiro Itaya, Hiroshi Yanagawa, and Yasubumi Sakakibara Isothermal Reactivating Whiplash PCR for Locally Programmable Molecular Computation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . John H. Reif and Urmi Majumder DNA as a Universal Substrate for Chemical Kinetics (Extended Abstract) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . David Soloveichik, Georg Seelig, and Erik Winfree A Simple DNA Gate Motif for Synthesizing Large-Scale Circuits (Extended Abstract) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lulu Qian and Erik Winfree Tiamat: A Three-Dimensional Editing Tool for Complex DNA Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sean Williams, Kyle Lund, Chenxiang Lin, Peter Wonka, Stuart Lindsay, and Hao Yan Connecting the Dots: Molecular Machinery for Distributed Robotics . . . . Yuriy Brun and Dustin Reishus Polyomino-Safe DNA Self-assembly via Block Replacement . . . . . . . . . . . . Chris Luhrs Robust Self-assembly of Graphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Stanislav Angelov, Sanjeev Khanna, and Mirk Visontai o Time Optimal Self-assembly for 2D and 3D Shapes: The Case of Squares and Cubes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Florent Becker, Eric Rmila, and Nicolas Schabanel e

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21

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Table of Contents

Self-assembly of Discrete Self-similar Fractals (Extended Abstract) . . . . . Matthew J. Patitz and Scott M. Summers Speeding Up Local-Search Type Algorithms for Designing DNA Sequences under Thermodynamical Constraints . . . . . . . . . . . . . . . . . . . . . Suguru Kawashimo, Yen Kaow Ng, Hirotaka Ono, Kunihiko Sadakane, and Masafumi Yamashita Sequentiality Induced by Spike Number in SNP Systems . . . . . . . . . . . . . . Oscar H. Ibarra, Andrei Pun, and Alfonso Rodrguez-Patn a o Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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